The most recent charges against eleven members of the church and two affiliated bodies include allegations of running a criminal organization and violating privacy rights. If the Church is convicted of the offences, it could face a total ban in the European nation.
The church's officials claim they represent a peaceful religion and deny all accusations. They argue the charges are meant to defame the Church's reputation.
"You can't explain an investigation this long and of such relentlessness against people who were only trying to peacefully practice their religion in Belgium," the spokesman for the group in Brussels, Eric Roux, told Agence France-Presse.
Federal prosecutor Christophe Caliman has asked the court to completely dissolve the Belgian branch and to levy a fine against it. The court heard final arguments on Friday, with a verdict expected in February.
Scientology was created by American science fiction author L. Ron Hubbard in the 1950s. It has been granted tax-exempt religious status in many countries including the US.
A Moscow court in November banned the local branch of the Church, backing the Russian Justice Ministry's claim that the organization's activity did not comply with federal laws on freedom of religion.